Perylene Bisimide Dimers as Fluorescent “Glue” for DNA and for Base‐Mismatch Detection

Abstract

Perylene-3,4:9,10-tetracarboxylic acid bisimide ("PB") and its derivatives are applied as fluorescent dyes in organic materials owing to their excellent photochemical stability as well as the high fluorescence quantum yields. [1,2] The strong hydrophobic stacking interactions between the PB chromophores make this dye an important building block for functional supramolecular architectures. [1,3] Based on these properties, PB in the dimeric form should be also of potential interest as a probe for fluorescent DNA/RNA analytics as well as for functionalized DNA-based architectures. Its noncovalent DNA-binding interactions have been studied with PB derivatives that had been modified with spermine [4] or other amines.[5] Moreover, an increasing number of publications about covalent modifications of oligonucleotides with PB have appeared over the last few years. [6][7][8][9][10][11][12] Recently, we presented a facile route for the synthetic incorporation of PB as an artificial DNA base in order to study the stacking interactions of this dye at specific sites in duplex DNA.[13]Herein, we present the evaluation of fluorescent PB dimers for the optical functionalization of DNA using three representative duplexes (DNA1, DNA3, and DNA4 a). For the synthetic modification of the corresponding oligonucleotides with the PB chromophore (Scheme 1), the 2-deoxyribofuranoside moiety was replaced by an acyclic linker system which is tethered to one of the imide nitrogens of the PB dye.[13] This linker allows the chromophore to intercalate in the base stack while providing high chemical stability during the automated phosphoramidite chemistry. [13,14] DNA1 bears one interstrand PB dimer inside the duplex, whereas DNA3 contains a PB monomer outside the duplex at each 5' end. Both duplexes contain palindromic sequences. When DNA1 and DNA3 are excited at 505 nm, the fluorescence spectra of both duplexes (Figure 1) are dominated by a broad band at % 660 nm without fine structure. This band corresponds to the excimer-type emission of the PB dimer that has been observed in nanoaggregates of perylene bisimides. [3,8,15] The UV/Vis spectra of DNA1 and DNA3 (Figure 2) at low temperatures show two major bands that are hyposochromically (506 nm) or bathochromically (545 nm) shifted in comparison to the 0!1 and 0!0 vibronic transitions of the PB monomer.[16] This result shows the strong p-p excitonic interactions of the two PB chromophores inside (DNA1) and outside (DNA3) of the duplex. [15] Both the excimer-type fluorescence band and the shifted absorption bands of DNA1 vanish at higher temperatures. It is remarkable that this occurs cooperatively at a temperature (75.9 8C) that corresponds to the cooperative thermal dehybridization of the whole DNA duplex, which is typically measured at 260 nm (T m = 78.6 8C). Apparently the intact helical duplex is required as a framework for the PB dimer formation. In comparison to the unmodified DNA2 (T m = 76.2 8C) the duplex DNA1 is stabilized by 2.4 8C through the Scheme 1. PB-modified duplexes DNA1-DNA3...

Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates

“…Indeed, upon binding the 3′ polyadenine tract of our constructs, the complementary strands would be expected to exhibit a relatively small effect on the rapid assembly dynamics and kinetics of the terminal PTCDI DNA base surrogates. Overall, Oligo1, Oligo2, and Oligo3 represented reasonable general analogues for the diverse class of perylene-modified oligonucleotides previously investigated with photophysical techniques in solution 16,17,19 and electrochemical techniques at solid substrates. 26 We characterized Oligo1, Oligo2, and Oligo3 with UV−vis spectroscopy (Figure 2), observing a clear evolution in the molecules' spectra as the number of PTCDI moieties increased.…”

Synthesis of DNA with Green Perylene Bisimides as DNA Base Substitutions

“…[16] We showed that perylene bisimide stacks as a chiral oligochromophore inside the double helical framework. [17] Moreover, we [9,17,19] and others [20] have shown that perylene bisimide triggers the reversible aggregation of complete DNA duplexes, hairpins, and dumbbells, yielding electronically conjugated nanostructures.…”

“…However, it is important to point out that in the absence of adjacent guanines the fluorescence intensity of PBI is still sufficient to obtain clear fluorescence readout for DNA assemblies [18][19][20] and bioanalysis. [16,17] With respect to the power of perylene bisimide in DNA-based nanostructuring it looked promising to design a new DNA base substitution based on the perylene bisimide scaffold that overcomes the problem of photoinduced guanine oxidation by maintaining the fluorescence quantum yield of PBI in guanine-poor sequences. Two strongly electron-donating substituents at the core of the chromophore should reduce the electron deficiency significantly and thus may prevent photoinduced guanine oxidation.…”

“…[17,21] None of the above-mentioned examples of DNA assemblies applied perylene bisimide modified at the core of the chromophore, the so-called bay area. This is surprising because both the optical and redox properties of perylene bisimide chromophores can be tuned signifi-cantly by introduction of substituents at the central carbocyclic scaffold.…”

Sensitive fluorescent sensing for DNA assay

“…Conventional methods that use radioactive [ 32 P]-labeled nucleic-acid (NA) probes or the polymerase-chain reaction (PCR) coupled with molecular fluorophore assays offer high sensitivity of detection, but they suffer from several drawbacks (e.g., complex handling procedures, easy contamination, high cost and lack of portability) [19][20][21][22]. Recently, great efforts have been made to develop biotechnologies to improve the sensitivity, the selectivity and the ease of operation for NA analysis [23][24][25][26][27][28][29][30][31][32][33].…”